The health and various ways to improve healthcare systems are one of the most concerns of human in history. By the growth of mobile technology, different mobile applications in the field of the healthcare system are developed. These mobile applications instantly gather and analyze the data of their users to help them in the health area. This volume of data will be a critical problem. Big data in healthcare mobile applications have its challenges and opportunities for the users and developers. Does this amount of gathered data which is increasing day by day can help the human to design new tools in healthcare systems and improve health condition? In this chapter, we will discuss meticulously the challenges and opportunities of big data in the healthcare mobile applications.